Sodium in PDB 7n5q: Peptide-Mhc Complex of Mouse H2-Db Presenting PA224 with E4C Mutation

The structure of Peptide-Mhc Complex of Mouse H2-Db Presenting PA224 with E4C Mutation, PDB code: 7n5q was solved by C.Szeto, S.Gras, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.32 / 1.76
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	46.41, 61.77, 71.68, 111.33, 91.19, 91.77
R / Rfree (%)	18 / 21.8

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Sodium atom in the Peptide-Mhc Complex of Mouse H2-Db Presenting PA224 with E4C Mutation (pdb code 7n5q). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 11 binding sites of Sodium where determined in the Peptide-Mhc Complex of Mouse H2-Db Presenting PA224 with E4C Mutation, PDB code: 7n5q:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 11 in the Peptide-Mhc Complex of Mouse H2-Db Presenting PA224 with E4C Mutation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Peptide-Mhc Complex of Mouse H2-Db Presenting PA224 with E4C Mutation within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:47.8 occ:1.00 OE2 A:GLU63 2.8 26.0 1.0 NE A:ARG62 3.1 59.9 1.0 NH2 A:ARG62 3.2 59.9 1.0 OG C:SER1 3.3 23.4 1.0 CZ A:ARG62 3.6 73.9 1.0 CD A:GLU63 3.8 30.0 1.0 CE2 A:TYR59 3.8 19.3 1.0 CZ2 A:TRP167 3.9 26.8 1.0 CH2 A:TRP167 3.9 25.8 1.0 CD2 A:TYR59 3.9 18.7 1.0 CB C:SER1 4.0 20.2 1.0 NZ A:LYS66 4.1 19.8 1.0 CE2 A:TRP167 4.2 27.4 1.0 CZ3 A:TRP167 4.3 25.2 1.0 CD A:ARG62 4.3 46.8 1.0 CG A:GLU63 4.3 16.7 1.0 CA C:SER1 4.5 17.2 1.0 CD2 A:TRP167 4.6 22.1 1.0 CE3 A:TRP167 4.6 23.6 1.0 CG A:ARG62 4.6 28.5 1.0 OE1 A:GLU63 4.7 20.3 1.0 CZ A:TYR59 4.8 19.9 1.0 NH1 A:ARG62 4.9 62.2 1.0 NE1 A:TRP167 4.9 25.6 1.0 CG A:TYR59 4.9 17.6 1.0

Sodium binding site 2 out of 11 in the Peptide-Mhc Complex of Mouse H2-Db Presenting PA224 with E4C Mutation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Peptide-Mhc Complex of Mouse H2-Db Presenting PA224 with E4C Mutation within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:32.1 occ:1.00 O A:GLU18 2.5 35.9 1.0 O A:ARG14 2.7 25.4 0.3 O A:ARG14 2.7 26.7 0.7 O A:HOH473 3.1 34.1 1.0 C A:GLU18 3.6 37.4 1.0 C A:ARG14 3.9 26.1 0.3 C A:ARG14 4.0 27.3 0.7 N A:GLU18 4.1 37.5 1.0 O A:HOH466 4.2 36.0 1.0 C A:PRO15 4.3 48.6 1.0 CA A:GLU18 4.4 37.0 1.0 O A:PRO15 4.5 39.7 1.0 N A:ARG14 4.6 21.3 0.3 N A:ARG14 4.6 23.6 0.7 N A:GLU19 4.7 30.5 1.0 CA A:PRO15 4.7 29.1 1.0 CB A:GLU18 4.8 38.7 1.0 N A:PRO15 4.8 23.8 1.0 CA A:ARG14 4.9 20.9 0.3 CA A:ARG14 4.9 23.8 0.7

Sodium binding site 3 out of 11 in the Peptide-Mhc Complex of Mouse H2-Db Presenting PA224 with E4C Mutation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Peptide-Mhc Complex of Mouse H2-Db Presenting PA224 with E4C Mutation within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:47.0 occ:1.00 O A:HOH501 2.7 28.8 1.0 CE B:LYS58 3.5 45.5 1.0 O B:HOH217 3.7 20.1 1.0 CD1 A:TYR27 4.0 15.1 1.0 CZ A:PHE8 4.0 13.5 1.0 ND2 A:ASN30 4.0 30.7 1.0 CE2 A:PHE8 4.1 16.0 1.0 CG A:TYR27 4.1 13.7 1.0 CE1 A:TYR27 4.1 16.2 1.0 CD2 A:TYR27 4.2 13.4 1.0 CZ A:TYR27 4.3 15.5 1.0 CE2 A:TYR27 4.4 12.8 1.0 CD B:LYS58 4.5 46.9 0.6 CA A:ASN30 4.5 17.9 1.0 NZ B:LYS58 4.6 27.5 1.0 CB A:ASN30 4.7 24.1 1.0 O A:ASN30 4.7 20.0 1.0 CB A:TYR27 4.8 11.9 1.0 CE1 A:PHE8 4.8 15.5 1.0 CG A:ASN30 4.8 44.1 1.0 CD2 A:PHE8 4.9 13.3 1.0 C A:ASN30 4.9 19.2 1.0 OH A:TYR27 5.0 14.7 1.0

Sodium binding site 4 out of 11 in the Peptide-Mhc Complex of Mouse H2-Db Presenting PA224 with E4C Mutation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Peptide-Mhc Complex of Mouse H2-Db Presenting PA224 with E4C Mutation within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:41.1 occ:1.00 O B:HOH263 2.6 33.4 1.0 NE2 A:HIS188 3.0 21.7 1.0 CG2 A:THR190 3.5 17.4 1.0 CE1 A:HIS188 3.8 21.4 1.0 CB B:PRO14 3.9 17.3 1.0 CD2 A:HIS188 4.1 21.9 1.0 O B:HOH276 4.3 36.8 1.0 O B:HOH215 4.3 32.4 1.0 CG B:PRO14 4.4 22.1 1.0 NE1 A:TRP204 4.5 15.3 1.0 CE2 A:TRP204 4.6 17.2 1.0 CA B:PRO14 4.8 15.4 1.0 CD1 A:TRP204 4.8 15.4 1.0 CB A:THR190 4.8 18.1 1.0 CZ2 A:TRP204 4.9 17.2 1.0 ND1 A:HIS188 5.0 21.3 1.0

Sodium binding site 5 out of 11 in the Peptide-Mhc Complex of Mouse H2-Db Presenting PA224 with E4C Mutation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Peptide-Mhc Complex of Mouse H2-Db Presenting PA224 with E4C Mutation within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:39.3 occ:1.00 O A:HOH451 2.5 27.9 1.0 O A:SER38 2.9 22.2 1.0 CG A:PRO43 3.6 33.0 1.0 C A:SER38 3.8 21.1 1.0 CB A:SER38 3.8 18.3 1.0 CA A:SER38 3.9 15.4 1.0 OE1 A:GLU71 4.1 35.4 1.0 CB A:PRO43 4.3 28.3 1.0 OE2 A:GLU71 4.4 36.7 1.0 NZ A:LYS68 4.7 55.0 0.9 CD A:PRO43 4.7 29.0 1.0 CD A:GLU71 4.7 37.6 1.0 OG A:SER38 4.8 19.1 1.0

Sodium binding site 6 out of 11 in the Peptide-Mhc Complex of Mouse H2-Db Presenting PA224 with E4C Mutation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Peptide-Mhc Complex of Mouse H2-Db Presenting PA224 with E4C Mutation within 5.0Å range: probe atom residue distance (Å) B Occ A:Na306 b:51.7 occ:1.00 O A:GLY237 3.4 20.4 1.0 C A:ASP238 3.6 21.6 1.0 N A:GLY239 3.7 16.5 1.0 CA A:ASP238 3.8 15.9 1.0 O A:ASP238 4.0 22.9 1.0 C A:GLY237 4.2 19.2 1.0 CA A:GLY239 4.3 17.4 1.0 N A:ASP238 4.4 15.9 1.0

Sodium binding site 7 out of 11 in the Peptide-Mhc Complex of Mouse H2-Db Presenting PA224 with E4C Mutation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Peptide-Mhc Complex of Mouse H2-Db Presenting PA224 with E4C Mutation within 5.0Å range: probe atom residue distance (Å) B Occ B:Na103 b:38.8 occ:1.00 O B:HOH247 2.8 25.7 1.0 CG1 B:ILE46 3.9 18.9 1.0 CD B:LYS41 4.1 24.1 1.0 CG2 B:ILE46 4.1 18.4 1.0 CA B:ILE46 4.2 17.5 1.0 CB B:ILE46 4.3 18.9 1.0 O B:HOH257 4.3 32.0 1.0 CB B:LYS41 4.5 19.4 1.0 CD1 B:ILE46 4.9 20.4 1.0 CG B:LYS41 4.9 16.1 1.0 O B:ARG45 5.0 24.8 1.0

Sodium binding site 8 out of 11 in the Peptide-Mhc Complex of Mouse H2-Db Presenting PA224 with E4C Mutation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Peptide-Mhc Complex of Mouse H2-Db Presenting PA224 with E4C Mutation within 5.0Å range: probe atom residue distance (Å) B Occ B:Na104 b:42.2 occ:1.00 ND2 B:ASN42 3.1 19.1 1.0 CB B:ASN42 3.8 20.7 1.0 CG B:ASN42 3.9 23.4 1.0 O B:LYS41 4.1 20.4 1.0 CG B:LYS41 4.2 16.1 1.0 CD B:LYS41 4.2 24.1 1.0 CE B:LYS41 4.3 28.5 1.0 C B:LYS41 4.6 21.1 1.0 NZ B:LYS41 4.8 32.4 1.0 OD1 B:ASP76 4.8 25.6 1.0 CA B:ASN42 4.9 19.7 1.0 CB B:LYS41 5.0 19.4 1.0

Sodium binding site 9 out of 11 in the Peptide-Mhc Complex of Mouse H2-Db Presenting PA224 with E4C Mutation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Peptide-Mhc Complex of Mouse H2-Db Presenting PA224 with E4C Mutation within 5.0Å range: probe atom residue distance (Å) B Occ F:Na301 b:50.0 occ:1.00 O F:GLU61 3.0 25.8 1.0 CG F:GLN65 3.6 53.2 1.0 N F:GLN65 3.7 22.0 1.0 CG F:GLU61 3.9 40.2 1.0 CG2 F:THR64 3.9 19.8 1.0 C F:GLU61 3.9 25.7 1.0 CB F:THR64 3.9 21.6 1.0 CA F:GLN65 4.1 21.2 1.0 CB F:GLN65 4.1 22.9 1.0 CA F:GLU61 4.1 23.8 1.0 C F:THR64 4.3 24.0 1.0 CB F:GLU61 4.6 25.4 1.0 CA F:THR64 4.6 19.6 1.0 OE1 F:GLN65 4.6 68.5 1.0 CD F:GLN65 4.6 72.1 1.0 O F:THR64 5.0 23.6 1.0

Sodium binding site 10 out of 11 in the Peptide-Mhc Complex of Mouse H2-Db Presenting PA224 with E4C Mutation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Peptide-Mhc Complex of Mouse H2-Db Presenting PA224 with E4C Mutation within 5.0Å range: probe atom residue distance (Å) B Occ G:Na102 b:38.8 occ:1.00 OD2 G:ASP59 2.8 29.9 1.0 CB G:ASP59 3.4 18.9 1.0 CG G:ASP59 3.5 25.4 1.0 OD1 G:ASP59 4.7 18.2 1.0 O G:HOH257 4.7 27.6 1.0 CA G:ASP59 4.9 16.9 1.0

C.Szeto, P.Zareie, R.C.Wirasinha, J.B.Zhang, A.T.Nguyen, A.Riboldi-Tunnicliffe, N.L.La Gruta, S.Gras, S.R.Daley. Covalent Tcr-Peptide-Mhc Interactions Induce T Cell Activation and Redirect T Cell Fate in the Thymus. Nat Commun V. 13 4951 2022.
ISSN: ESSN 2041-1723
PubMed: 35999236
DOI: 10.1038/S41467-022-32692-4